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Can Agricultural Management Induced Changes in Soil Organic Carbon Be Detected Using Mid-Infrared Spectroscopy?
Get PDFA major limitation to building credible soil carbon sequestration programs is the cost of measuring soil carbon change. Diffuse reflectance spectroscopy (DRS) is considered a viable low-cost alternative to traditional laboratory analysis of soil organic carbon (SOC). While numerous studies have shown that DRS can produce accurate and precise estimates of SOC across landscapes, whether DRS can detect subtle management induced changes in SOC at a given site has not been resolved. Here, we leverage archived soil samples from seven long-term research trials in the U.S. to test this question using mid infrared (MIR) spectroscopy coupled with the USDA-NRCS Kellogg Soil Survey Laboratory MIR spectral library. Overall, MIR-based estimates of SOC%, with samples scanned on a secondary instrument, were excellent with the root mean square error ranging from 0.10 to 0.33% across the seven sites. In all but two instances, the same statistically significant (p \u3c 0.10) management effect was found using both the lab-based SOC% and MIR estimated SOC% data. Despite some additional uncertainty, primarily in the form of bias, these results suggest that large existing MIR spectral libraries can be operationalized in other laboratories for successful carbon monitoring
Detection and quantification of γ-H2AX using a dissociation enhanced lanthanide fluorescence immunoassay
Get PDFPhosphorylation of the histone protein H2AX to form γ-H2AX foci directly represents DNA double-strand break formation. Traditional γ-H2AX detection involves counting individual foci within individual nuclei. The novelty of this work is the application of a time-resolved fluorescence assay using dissociation-enhanced lanthanide fluorescence immunoassay for quantitative measurements of γ-H2AX. For comparison, standard fluorescence detection was employed and analyzed either by bulk fluorescent measurements or by direct foci counting using BioTek Spot Count algorithm and Gen 5 software. Etoposide induced DNA damage in A549 carcinoma cells was compared across all test platforms. Time resolved fluorescence detection of europium as a chelated complex enabled quantitative measurement of γ-H2AX foci with nanomolar resolution. Comparative bulk fluorescent signals achieved only micromolar sensitivity. Lanthanide based immunodetection of γ-H2AX offers superior detection and a user-friendly workflow. These approaches have the potential to improve screening of compounds that either enhance DNA damage or protect against its deleterious effects
Virus-Targeted Transcriptomic Analyses Implicate Ranaviral Interaction with Host Interferon Response in Frog Virus 3-Infected Frog Tissues
Get PDFRanaviruses (Iridoviridae), including Frog Virus 3 (FV3), are large dsDNA viruses that cause devastating infections globally in amphibians, fish, and reptiles, and contribute to catastrophic amphibian declines. FV3’s large genome (~105 kb) contains at least 98 putative open reading frames (ORFs) as annotated in its reference genome. Previous studies have classified these coding genes into temporal classes as immediate early, delayed early, and late viral transcripts based on their sequential expression during FV3 infection. To establish a high-throughput characterization of ranaviral gene expression at the genome scale, we performed a whole transcriptomic analysis (RNA-Seq) using total RNA samples containing both viral and cellular transcripts from FV3-infected Xenopus laevis adult tissues using two FV3 strains, a wild type (FV3-WT) and an ORF64R-deleted recombinant (FV3-∆64R). In samples from the infected intestine, liver, spleen, lung, and especially kidney, an FV3-targeted transcriptomic analysis mapped reads spanning the full-genome coverage at ~10× depth on both positive and negative strands. By contrast, reads were only mapped to partial genomic regions in samples from the infected thymus, skin, and muscle. Extensive analyses validated the expression of almost all of the 98 annotated ORFs and profiled their differential expression in a tissue-, virus-, and temporal class-dependent manner. Further studies identified several putative ORFs that encode hypothetical proteins containing viral mimicking conserved domains found in host interferon (IFN) regulatory factors (IRFs) and IFN receptors. This study provides the first comprehensive genome-wide viral transcriptome profiling during infection and across multiple amphibian host tissues that will serve as an instrumental reference. Our findings imply that Ranaviruses like FV3 have acquired previously unknown molecular mimics, interfering with host IFN signaling during evolution
California Legacy Survey. II. Occurrence of Giant Planets beyond the Ice Line
Get PDFWe used high-precision radial velocity measurements of FGKM stars to determine the occurrence of giant planets as a function of orbital separation spanning 0.03–30 au. Giant planets are more prevalent at orbital distances of 1–10 au compared to orbits interior or exterior of this range. The increase in planet occurrence at ∼1 au by a factor of ∼4 is highly statistically significant. A fall-off in giant planet occurrence at larger orbital distances is favored over models with flat or increasing occurrence. We measure giant planets per 100 stars with semimajor axes of 2–8 au and giant planets per 100 stars in the range 8–32 au, a decrease in occurrence with increasing orbital separation that is significant at the ∼2σ level. We find that the occurrence rate of sub-Jovian planets (0.1–1 Jupiter masses) is also enhanced for 1–10 au orbits. This suggests that lower-mass planets may share the formation or migration mechanisms that drive the increased prevalence near the water–ice line for their Jovian counterparts. Our measurements of cold gas giant occurrence are consistent with the latest results from direct imaging surveys and gravitational lensing surveys despite different stellar samples. We corroborate previous findings that giant planet occurrence increases with stellar mass and metallicity
How much has the Sun influenced Northern Hemisphere temperature trends? An ongoing debate
Get PDFIn order to evaluate how much Total Solar Irradiance (TSI) has influenced Northern Hemisphere surface air temperature trends, it is important to have reliable estimates of both quantities. Sixteen different estimates of the changes in TSI since at least the 19th century were compiled from the literature. Half of these estimates are low variability and half are high variability . Meanwhile, five largely-independent methods for estimating Northern Hemisphere temperature trends were evaluated using: 1) only rural weather stations; 2) all available stations whether urban or rural (the standard approach); 3) only sea surface temperatures; 4) tree-ring widths as temperature proxies; 5) glacier length records as temperature proxies. The standard estimates which use urban as well as rural stations were somewhat anomalous as they implied a much greater warming in recent decades than the other estimates, suggesting that urbanization bias might still be a problem in current global temperature datasets – despite the conclusions of some earlier studies. Nonetheless, all five estimates confirm that it is currently warmer than the late 19th century, i.e., there has been some global warming since the 19th century. For each of the five estimates of Northern Hemisphere temperatures, the contribution from direct solar forcing for all sixteen estimates of TSI was evaluated using simple linear least-squares fitting. The role of human activity on recent warming was then calculated by fitting the residuals to the UN IPCC\u27s recommended anthropogenic forcings time series. For all five Northern Hemisphere temperature series, different TSI estimates suggest everything from no role for the Sun in recent decades (implying that recent global warming is mostly human-caused) to most of the recent global warming being due to changes in solar activity (that is, that recent global warming is mostly natural). It appears that previous studies (including the most recent IPCC reports) which had prematurely concluded the former, had done so because they failed to adequately consider all the relevant estimates of TSI and/or to satisfactorily address the uncertainties still associated with Northern Hemisphere temperature trend estimates. Therefore, several recommendations on how the scientific community can more satisfactorily resolve these issues are provided
The Hubble PanCET program: long-term chromospheric evolution and flaring activity of the M dwarf host GJ 3470★
Get PDFNeptune-size exoplanets seem particularly sensitive to atmospheric evaporation, making it essential to characterize the stellar high-energy radiation that drives this mechanism. This is particularly important with M dwarfs, which emit a large and variable fraction of their luminosity in the ultraviolet and can display strong flaring behavior. The warm Neptune GJ 3470b, hosted by an M2 dwarf, was found to harbor a giant exosphere of neutral hydrogen thanks to three transits observed with the Hubble Space Telescope Imaging Spectrograph (HST/STIS). Here we report on three additional transit observations from the Panchromatic Comparative Exoplanet Treasury program, obtained with the HST Cosmic Origin Spectrograph. These data confirm the absorption signature from GJ 3470b’s exosphere in the stellar Lyman-α line and demonstrate its stability over time. No planetary signatures are detected in other stellar lines, setting a 3σ limit on GJ 3470b’s far-ultraviolet (FUV) radius at 1.3 times its Roche lobe radius. We detect three flares from GJ 3470. They show different spectral energy distributions but peak consistently in the Si III line, which traces intermediate-temperature layers in the transition region. These layers appear to play a particular role in GJ 3470’s activity as emission lines that form at lower or higher temperatures than Si III evolved differently over the long term. Based on the measured emission lines, we derive synthetic X-ray and extreme-ultraviolet (X+EUV, or XUV) spectra for the six observed quiescent phases, covering one year, as well as for the three flaring episodes. Our results suggest that most of GJ 3470’s quiescent high-energy emission comes from the EUV domain, with flares amplifying the FUV emission more strongly. The neutral hydrogen photoionization lifetimes and mass loss derived for GJ 3470b show little variation over the epochs, in agreement with the stability of the exosphere. Simulations informed by our XUV spectra are required to understand the atmospheric structure and evolution of GJ 3470b and the role played by evaporation in the formation of the hot-Neptune desert
A Methyl Esterase 1 (PvMES1) Promotes the Salicylic Acid Pathway and Enhances Fusarium Wilt Resistance in Common Beans
Get PDFCommon bean (Phaseolus vulgaris L.) is an important food legume. Fusarium wilt caused by Fusarium oxysporum f. sp. phaseoli is one of the most serious soil-born diseases of common bean found throughout the world and affects the yield and quality of the crop. Few sources of Fusarium wilt resistance exist in legumes and most are of quantitative inheritance. In this study, we have identified a methyl salicylate esterase (MES), PvMES1, that contributes to plant defense response by regulating the salicylic acid (SA) mediated signaling pathway in response to Fusarium wilt in common beans. The result showed the role of PvMES1 in regulating SA levels in common bean and thus the SA signaling pathway and defense response mechanism in the plant. Overexpression of the PvMES1 gene enhanced Fusarium wilt resistance; while silencing of the gene caused susceptibility to the diseases. RNA-seq analysis with these transiently modified plants showed that genes related to SA level changes included the following gene ontologies: a) interaction between host and pathogen; b) phenylpropanoid synthesis; and c) sugar metabolism as well as others. These key signal elements activated the defense response pathway in common bean to Fusarium wilt. Collectively, our findings indicate that PvMES1 plays a pivotal role in regulating SA biosynthesis and signaling, and increasing Fusarium wilt resistance in common bean, thus providing novel insight into the practical applications of both SA and MES genes and pathways they contribiute to for developing elite crop varieties with enhanced broad-spectrum resistance to this critical disease
Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions
Get PDFAmaranthus is a genus of C4 dicotyledonous herbaceous plants, and three New World species have been domesticated to produce grain crops with light colored seed which are classified as pseudo-cereals rich in protein and minerals. A core collection of grain amaranths and immediate precursor species has been established, representing the closest related species. The goal of this study was to evaluate the genetic diversity in that collection of cultivated and wild species, using competitive allele single nucleotide polymorphism markers. A secondary objective was to determine the relationships among the three cultivated species and non-domesticated Amaranthus, while a third objective was to evaluate the utility of the markers in detecting diversity in the 276 genotypes. The markers were found to be highly variable with an average polymorphism information content of 0.365. All markers were bi-allelic; and the major allele frequency ranged from 0.388 to 0.871. Population structure analysis of the cultigens revealed the presence of two sub populations. Phylogeny confirmed that the two Mesoamerican species, Amaranthus cruentus and Amaranthus hypochondriacus, were related and distant from the South American species Amaranthus caudatus, which in turn was very closely clustered with Amaranthus quitensis, even though this is considered a weedy relative. The first pair of species were likely to have inter-crossed, while the latter two likely exist in a wild-cultivated hybrid state. In conclusion, the results of this SNP study provided insights on amaranth cultivars and their relationship to wild species, the probable domestication events leading to the cultivars, and possible crop breeding or germplasm conservation strategies
Effect of High Intensity Ultraviolet Light (UV-A) Emitting Diodes Technology on the Reduction of Mycotoxins in Whole Milk: Kinetic and Cytotoxicity Study
No full textThe effectiveness of a UV-A light emitting diode system (LED) to reduce the concentrations of aflatoxin B1, aflatoxin M1 (AFB1, AFM1) in whole milk (WM) was investigated. Irradiation experiments were conducted using an LED system operating at 365 nm. Known concentrations of aflatoxins were spiked in WM and irradiated at quantified UV doses which was calculated based on the average volumetric intensity. LC-MS product ion scans were used to identify and semi-quantify photodegraded products of AFB1 and AFM1. It was observed that UV irradiation significantly reduced aflatoxins in WM (p \u3c 0.05). In comparison to control, the maximum UV-A exposure reduced AFB1 and AFM1 concentrations to 78.2 ± 2.36 % (at 836 mJ/cm2) and 65.7 ± 1.65% (at 857 mJ/cm2), respectively. In cytotoxicity studies, our results demonstrated that the increase in UV-A dosage decreased the aflatoxins-induced cytotoxicity in HepG2 cells, and no significant aflatoxin-induced cytotoxicity was observed at the highest given UV-A irradiation of 777 (AFB1), 838 (AFM1), and 746 (total AFs) mJ/cm2. Tryptophan (TRP), glutamic acid (GLU), lysine (LYS), glutamine (GLN) and lipid peroxidation were assessed in UV-A irradiated WM. No significant reduction in amino acids was observed, p\u3e0.05. At 279 mJ/cm2 no significant lipid peroxidation was observed. In contrast, minor changes lipid peroxidation was observed 838 mJ/cm2, p\u3c0.05. The volatile profiling showed that alcohols, the key contributor of oxidized flavor was not significantly affected by the UV-A irradiation. Western blotting was used to assess the effect of UV-A irradiated WM on protein expression in HepG2 cells. Because the targeted gene p53 was not considerably altered, we can affirm that UV-A irradiated WM was safe from toxins that leads to oxidative cell stress. This is indicating substantial breakdown of AF in WM by UV-A as well as no accumulation of toxic components from protein, lipid, and FAA degradation. This study clearly demonstrated the efficacy of UV-A LED system in reducing AF in WM below Food and Drug Administration recommended limits. Investigating the cytotoxicity, and mutagenicity of UV exposed aflatoxins in WM using animal model is warranted in the future